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      Cryo-EM structure of the Ebola virus nucleoprotein–RNA complex at 3.6 Å resolution

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          Helical reconstruction in RELION

          We describe a new implementation for the reconstruction of helical assemblies in the empirical Bayesian framework of RELION. Our approach calculates optimal linear filters for the 3D reconstruction by embedding helical symmetry operators in Fourier-space, and deals with deviations from perfect helical symmetry through Gaussian-shaped priors on the orientations of individual segments. By incorporating our approach into the standard pipeline for single-particle analysis in RELION, our implementation aims to be easily accessible for non-experienced users. Although our implementation does not solve the problem that grossly incorrect structures can be obtained when the wrong helical symmetry is imposed, we show for four different test cases that it is capable of reconstructing structures to near-atomic resolution.
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            Structure and assembly of the Ebola virus nucleocapsid

            Ebola and Marburg viruses are filoviruses: filamentous, enveloped viruses that cause hemorrhagic fever1. Filoviruses are within the order Mononegavirales2 which also includes rabies virus, measles virus, and respiratory syncytial virus. Mononegaviruses have non-segmented, single-stranded negative-sense RNA genomes that are encapsidated by nucleoprotein (NP) and other viral proteins to form a helical nucleocapsid (NC). NC acts as a scaffold for virus assembly and as a template for genome transcription and replication. Insights into NP-NP interactions have been derived from structural studies of oligomerized, RNA-encapsidating NP3–6 and cryo-electron microscopy (cryo-EM) of NC7–12 or NC-like structures11–13. There have been no high-resolution reconstructions of complete mononegavirus NCs. Here, we have applied cryo-electron tomography and subtomogram averaging to determine the structure of Ebola virus NC within intact viruses and recombinant NC-like assemblies. These structures reveal the identity and arrangement of the NC components, and suggest that the formation of an extended alpha-helix from the disordered C-terminal region of NP-core links NP oligomerization, NC condensation, RNA encapsidation, and accessory protein recruitment.
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              The Uppsala Electron-Density Server.

              The Uppsala Electron Density Server (EDS; http://eds.bmc.uu.se/) is a web-based facility that provides access to electron-density maps and statistics concerning the fit of crystal structures and their maps. Maps are available for approximately 87% of the crystallographic Protein Data Bank (PDB) entries for which structure factors have been deposited and for which straightforward map calculations succeed in reproducing the published R value to within five percentage points. Here, an account is provided of the methods that are used to generate the information contained in the server. Some of the problems that are encountered in the map-generation process as well as some spin-offs of the project are also discussed.
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                Author and article information

                Journal
                Nature
                Nature
                Springer Nature America, Inc
                0028-0836
                1476-4687
                October 17 2018
                Article
                10.1038/s41586-018-0630-0
                30333622
                e97abc7a-0be3-4fda-b4b4-16dd7dfc4d27
                © 2018

                http://www.springer.com/tdm

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